Merge tag '9.6.beta0' into t/32927/pkgs_sagemath_standard_setup_py__m…

…ove_distributions_logic_to_a_new_package_sagemath_optional

SageMath version 9.6.beta0, Release Date: 2022-02-06

.github/workflows/ticket.yaml

@@ -0,0 +1,31 @@
+# CI Test For Individual Tickets
+
+name: Ticket CI
+
+on:
+  push:
+    branches:
+      # Once set to positive review, the branch from the trac ticket
+      # number 12345 will be copied to ticket/12345
+      - 'ticket/**'
+
+
+jobs:
+  ticket_ci:
+
+    # TODO: this action is only a placeholder, github actions needs
+    # this in the master branch to enable it
+
+    name: Ticket CI
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Install pycodestyle
+      run: pip install tox pycodestyle
+    - name: Lint using pycodestyle
+      run: tox -e pycodestyle-minimal

.github/workflows/tox-experimental.yml

@@ -83,6 +83,7 @@ jobs:
             fi
             if echo "$TOKEN" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin; then
               echo "DOCKER_PUSH_REPOSITORY=docker.pkg.github.com/${{ github.repository }}/" >> $GITHUB_ENV
+              echo "DOCKER_CONFIG_FILE=$HOME/.docker/config.json" >> $GITHUB_ENV
             fi
       - run: |
           set -o pipefail; EXTRA_DOCKER_BUILD_ARGS="--build-arg USE_MAKEFLAGS=\"-k V=0 SAGE_NUM_THREADS=3\"" tox -e $TOX_ENV -- $TARGETS 2>&1 | sed "/^configure: notice:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: warning:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: error:/s|^|::error file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;"

.github/workflows/tox-optional.yml

@@ -83,6 +83,7 @@ jobs:
             fi
             if echo "$TOKEN" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin; then
               echo "DOCKER_PUSH_REPOSITORY=docker.pkg.github.com/${{ github.repository }}/" >> $GITHUB_ENV
+              echo "DOCKER_CONFIG_FILE=$HOME/.docker/config.json" >> $GITHUB_ENV
             fi
       - run: |
           set -o pipefail; EXTRA_DOCKER_BUILD_ARGS="--build-arg USE_MAKEFLAGS=\"-k V=0 SAGE_NUM_THREADS=3\"" tox -e $TOX_ENV -- $TARGETS 2>&1 | sed "/^configure: notice:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: warning:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: error:/s|^|::error file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;"

.github/workflows/tox.yml

@@ -76,6 +76,7 @@ jobs:
             fi
             if echo "$TOKEN" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin; then
               echo "DOCKER_PUSH_REPOSITORY=docker.pkg.github.com/${{ github.repository }}/" >> $GITHUB_ENV
+              echo "DOCKER_CONFIG_FILE=$HOME/.docker/config.json" >> $GITHUB_ENV
             fi
       - run: |
           set -o pipefail; EXTRA_DOCKER_BUILD_ARGS="--build-arg USE_MAKEFLAGS=\"-k V=0 SAGE_NUM_THREADS=3\"" tox -e $TOX_ENV -- $TARGETS 2>&1 | sed "/^configure: notice:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: warning:/s|^|::warning file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;/^configure: error:/s|^|::error file=artifacts/$LOGS_ARTIFACT_NAME/config.log::|;"

.gitignore

@@ -163,6 +163,14 @@ build/bin/sage-build-env-config
 /pkgs/*/*.egg-info
 /pkgs/*/.tox
 
+/pkgs/sagemath-objects/setup.cfg
+/pkgs/sagemath-categories/setup.cfg
+/pkgs/sagemath-objects/pyproject.toml
+/pkgs/sagemath-categories/pyproject.toml
+/pkgs/sagemath-objects/requirements.txt
+/pkgs/sagemath-categories/requirements.txt
+/pkgs/sagemath-categories/MANIFEST.in
+
 # same for old locations - before Trac #31577
 /build/pkgs/*/src/build
 /build/pkgs/*/src/dist

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.5.rc3", 
-    "version": "9.5.rc3", 
+    "title": "sagemath/sage: 9.6.beta0", 
+    "version": "9.6.beta0", 
     "upload_type": "software", 
-    "publication_date": "2022-01-18", 
+    "publication_date": "2022-02-06", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.5.rc3", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.6.beta0", 
             "relation": "isSupplementTo"
         }, 
         {

Makefile

@@ -85,6 +85,8 @@ pypi-sdists: sage_setup
 	./sage --sh build/pkgs/sage_docbuild/spkg-src
 	./sage --sh build/pkgs/sage_setup/spkg-src
 	./sage --sh build/pkgs/sagelib/spkg-src
+	./sage --sh build/pkgs/sagemath_objects/spkg-src
+	./sage --sh build/pkgs/sagemath_categories/spkg-src
 	@echo "Built sdists are in upstream/"
 
 # ssl: build Sage, and also install pyOpenSSL. This is necessary for
@@ -228,7 +230,7 @@ PTESTALL = ./sage -t -p --all
 # When the documentation is installed, "optional" also includes all tests marked 'sagemath_doc_html',
 # see https://trac.sagemath.org/ticket/25345, https://trac.sagemath.org/ticket/26110, and
 # https://trac.sagemath.org/ticket/32759
-TESTALL_FLAGS = --optional=sage,optional,external,build
+TESTALL_FLAGS = --optional=sage,optional,external
 
 test: all
 	$(TESTALL) --logfile=logs/test.log

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.5.rc3, Release Date: 2022-01-18
+SageMath version 9.6.beta0, Release Date: 2022-02-06

build/make/Makefile.in

@@ -184,7 +184,7 @@ AM_V_at =
 endif
 
 # Trac #33125: Handle make options -n, -t, -q
-ifeq ($(foreach flag, n t q, $(findstring $(flag),$(filter-out --%,$(MAKEFLAGS)))),)
+ifeq ($(strip $(foreach flag,n t q,$(findstring $(flag),$(filter-out --%,$(MAKEFLAGS))))),)
 PLUS = +
 else
 PLUS =

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=82db5472ac5d29950254ec45b1f448dbc4f8e9f0
-md5=92c171e5c495c2c2f601d49f89cdaa36
-cksum=3258581436
+sha1=345924fc41ea858557c397fb38060606c868b0bd
+md5=2e5d32301a1c1debf4ec508ebc157ec2
+cksum=1618326589

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-ad7e1731c0dd97d79084a0c3baa0022ba4cfff69
+f0df3d8b40169709426fd20a9f71cdcb30851c90

build/pkgs/cryptominisat/SPKG.rst

@@ -35,3 +35,4 @@ Special Update/Build Instructions
 
 CryptoMiniSat's tarball downloaded from github is called VERSION.tar.gz
 and should be renamed to cryptominisat-VERSION.tar.gz
+Its Python module is installed by the pycryptosat spkg.

build/pkgs/cryptominisat/spkg-install.in

@@ -3,7 +3,3 @@ cd src
 sdh_cmake -DUSE_GAUSS='ON' $EXTRA_OPTS
 sdh_make VERBOSE=ON
 sdh_make_install VERBOSE=ON
-
-cd pycryptosat
-
-sdh_pip_install .

build/pkgs/cython/checksums.ini

@@ -1,5 +1,5 @@
 tarball=Cython-VERSION.tar.gz
-sha1=21187175b7da94020e662c04f805d580f1071880
-md5=81aff945f5bfdfb86e7a5d24f5467668
-cksum=2423037501
+sha1=bda825a34f18c11889562466264e29a8cb0e8806
+md5=1e1edbb3d41e0e5a0eec98288ce113f2
+cksum=169454778
 upstream_url=https://pypi.io/packages/source/C/Cython/Cython-VERSION.tar.gz

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-0.29.24
+0.29.25

build/pkgs/igraph/checksums.ini

@@ -1,5 +1,5 @@
 tarball=igraph-VERSION.tar.gz
-sha1=754908e45b31883107b802470779310cbb7c64d4
-md5=b063648d9a0a8de11b3fa886837f1819
-cksum=3580664179
+sha1=34aa12fbb76bf383e6c80d3935351d63b7d09c10
+md5=81f181c39a066075acb8aa0a087b97a0
+cksum=1808520323
 upstream_url=https://github.com/igraph/igraph/releases/download/VERSION/igraph-VERSION.tar.gz

build/pkgs/igraph/dependencies

@@ -1,4 +1,4 @@
-$(MP_LIBRARY) glpk $(BLAS) libxml2
+$(MP_LIBRARY) glpk $(BLAS) libxml2 suitesparse | cmake
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/igraph/package-version.txt

@@ -1 +1 @@
-0.8.3
+0.9.5

build/pkgs/igraph/spkg-install.in

@@ -1,5 +1,21 @@
 export CFLAGS="$CFLAGS -Wno-strict-prototypes -Wno-implicit-function-declaration"
 cd src
-sdh_configure --with-external-blas --with-external-lapack --with-external-glpk
+mkdir build
+cd build
+# https://igraph.org/c/doc/igraph-Installation.html
+sdh_cmake -DCMAKE_VERBOSE_MAKEFILE=ON \
+          -DBUILD_STATIC_LIBS=OFF \
+          -DBUILD_SHARED_LIBS=ON \
+          -DIGRAPH_USE_INTERNAL_GLPK=OFF \
+          -DIGRAPH_USE_INTERNAL_GMP=OFF \
+          -DBLA_VENDOR=OpenBLAS \
+          -DBLAS_LIBRARIES="$(pkg-config --libs blas)" \
+          -DLAPACK_LIBRARIES="$(pkg-config --libs lapack)" \
+          -DIGRAPH_USE_INTERNAL_BLAS=OFF \
+          -DIGRAPH_USE_INTERNAL_LAPACK=OFF \
+          -DIGRAPH_USE_INTERNAL_SUITESPARSE=OFF \
+          -DIGRAPH_GLPK_SUPPORT=ON \
+          -DIGRAPH_GRAPHML_SUPPORT=ON \
+          ..
 sdh_make
-sdh_make_install -j1
+sdh_make_install

build/pkgs/pari_jupyter/SPKG.rst

@@ -0,0 +1,27 @@
+pari_jupyter: A Jupyter kernel for PARI/GP
+==========================================
+
+Description
+-----------
+
+A Jupyter kernel for PARI/GP
+
+License
+-------
+
+GPL version 3 or later
+
+
+Upstream Contact
+----------------
+
+-  https://github.com/sagemath/pari-jupyter
+
+Dependencies
+------------
+
+-  Python >= 3.6.1
+-  Jupyter 4
+-  PARI version 2.13 or later
+-  Readline (any version which works with PARI)
+-  Optional: Cython version 0.25 or later

build/pkgs/pari_jupyter/checksums.ini

@@ -0,0 +1,5 @@
+tarball=pari-jupyter-VERSION.tar.gz
+sha1=442ab166c9229df1ad1b40e26fb6d0c23b8282f4
+md5=2fdaa74ca8502aa8832c4c3eeb49d8c3
+cksum=1047550915
+upstream_url=https://pypi.io/packages/source/p/pari_jupyter/pari-jupyter-VERSION.tar.gz

build/pkgs/pari_jupyter/dependencies

@@ -0,0 +1 @@
+$(PYTHON) pari | $(PYTHON_TOOLCHAIN) cython notebook jupyter_core

build/pkgs/pari_jupyter/distros/conda.txt

@@ -0,0 +1 @@
+pari_jupyter

build/pkgs/pari_jupyter/distros/repology.txt

@@ -0,0 +1,2 @@
+pari-jupyter
+python:pari-jupyter

build/pkgs/pari_jupyter/install-requires.txt

@@ -0,0 +1 @@
+pari_jupyter >=1.3.2

build/pkgs/pari_jupyter/package-version.txt

@@ -0,0 +1 @@
+1.4.0

build/pkgs/pari_jupyter/spkg-install.in

@@ -0,0 +1 @@
+cd src && sdh_pip_install .

build/pkgs/pari_jupyter/type

@@ -0,0 +1 @@
+optional

build/pkgs/pycryptosat/SPKG.rst

@@ -0,0 +1,22 @@
+pycryptosat: Python module of cryptominisat
+===========================================
+
+Description
+-----------
+
+   Build and install pycryptosat into appropriate venv.
+   See cryptominisat for more details.
+
+License
+-------
+
+MIT License
+
+
+Upstream Contact
+----------------
+
+-  Authors: Mate Soos
+-  Email: soos.mate@gmail.com
+-  Website: http://www.msoos.org/
+-  Releases: https://github.com/msoos/cryptominisat/releases

build/pkgs/pycryptosat/checksums.ini

@@ -0,0 +1 @@
+../cryptominisat/checksums.ini

build/pkgs/pycryptosat/dependencies

@@ -0,0 +1,5 @@
+$(PYTHON) m4ri zlib libpng cryptominisat | cmake boost_cropped $(PYTHON_TOOLCHAIN)
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/pycryptosat/distros/conda.txt

@@ -0,0 +1 @@
+cryptominisat

build/pkgs/pycryptosat/distros/homebrew.txt

@@ -0,0 +1 @@
+cryptominisat

build/pkgs/pycryptosat/distros/repology.txt

@@ -0,0 +1 @@
+cryptominisat

build/pkgs/pycryptosat/install-requires.txt

@@ -0,0 +1 @@
+pycryptosat

build/pkgs/pycryptosat/package-version.txt

@@ -0,0 +1 @@
+5.6.8

build/pkgs/pycryptosat/spkg-install.in

@@ -0,0 +1,7 @@
+cd src
+
+sdh_cmake -DUSE_GAUSS='ON' $EXTRA_OPTS
+
+cd pycryptosat
+
+sdh_pip_install .

build/pkgs/pycryptosat/type

@@ -0,0 +1 @@
+optional

build/pkgs/python_igraph/checksums.ini

@@ -1,5 +1,5 @@
 tarball=python-igraph-VERSION.tar.gz
-sha1=c54c5f5b533979f93172b75e422508973e6a4f54
-md5=dcc3b722a9772b43a769940815c501f7
-cksum=794576917
-upstream_url=https://github.com/igraph/python-igraph/releases/download/VERSION/python-igraph-VERSION.tar.gz
+sha1=42f92301e3a02bc1bb9d8ceb15dd31a350863cb5
+md5=047e02f58142210a26c190ed6b617aef
+cksum=3702659607
+upstream_url=https://pypi.io/packages/source/i/igraph/igraph-VERSION.tar.gz

build/pkgs/python_igraph/install-requires.txt

@@ -1 +1 @@
-python_igraph >=0.7.1999
+igraph

build/pkgs/python_igraph/package-version.txt

@@ -1 +1 @@
-0.8.3
+0.9.8

build/pkgs/sage_setup/install-requires.txt

@@ -1 +1 @@
-sage-setup
+sage-setup ~= 9.5.b6